Targeting dna-pkcs and b7-h1 to treat cancer

ABSTRACT

Materials and methods for treating potentially chemoresistant tumors (e.g., using DNA-PKcs inhibitors and anti-B7-H1 antibodies) are provided herein.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. Utility application Ser. No. 16/681,154, filed Nov. 12, 2019, now U.S. Pat. No. 11,504,376, which is a continuation of U.S. application Ser. No. 15/325,612, filed Jan. 11, 2017, now U.S. Pat. No. 10,517,875, which is a National Stage application under 35 U.S.C. § 371 of International Application No. PCT/US2015/032016 having an International Filing Date of May 21, 2015, which claims benefit of priority from U.S. Provisional Application No. 62/027,841, filed on Jul. 23, 2014. The disclosures of the prior applications are considered part of (and are incorporated by reference in) the disclosure of this application.

SEQUENCE LISTING

This application contains a Sequence Listing that has been submitted electronically as an XML file named 07039-1359003_SL_ST26.xml. The XML file, created on Nov. 21, 2022, is 22,999 bytes in size. The material in the XML file is hereby incorporated by reference in its entirety.

TECHNICAL FIELD

This document relates to materials and methods for treating potentially chemoresistant tumors, and particularly to materials and methods for treating such tumors with DNA-PKcs inhibitors.

BACKGROUND

The development of resistance to chemotherapy and immunotherapy is a major obstacle in prolonging survival of cancer patients. The emergence of chemoresistance and immunoresistance were traditionally viewed as parallel and unrelated events, but more recent evidence indicates that overexpression of some immune checkpoint molecules may negatively influence antitumor immunity and also render tumor cells resistant to chemotherapeutic agents (Tamura et al., Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, UK 27:464-472, 2013; Ghebeh et al., Breast Cancer Res 12:R48, 2010; and Liu et al., Molecular Cancer Ther 10:960-971, 2011).

SUMMARY

Cancer therapies using checkpoint blockades can blunt the immune-suppressive function of ligands (e.g., B7-H1 on tumor cells) by blocking interaction with their receptors (e.g., PD-1 on T cells) (Zang and Allison, Clin Cancer Res 13:5271-5279, 2007; and Dong and Chen, J Mol Med 81:281-287, 2003). While such therapies can contribute to enhanced antitumor immunity, blocking the binding of B7-H1 to PD-1 may not overcome B7-H1-mediated chemoresistance.

The therapeutic methods described herein can be used to target B7-H1's intrinsic signaling pathway in relation to chemoresistance. These methods are based on the results of experiments that elucidated a molecular mechanism underlying B7-H1-mediated tumor chemoresistance, as described below, thus providing new therapeutic targets to defuse this mechanism. For example, this document is based at least in part on the discovery that DNA-PKcs is a B7-H1 binding protein, and that DNA-PKcs can be targeted to reduce B7-H1-mediated chemoresistance. This discovery was unexpected, as DNA-PKcs is a nuclear protein involved in DNA damage repair (Collis et al., Oncogene 24:949-961, 2005), while B7-H1 is an immunoregulatory molecule mainly expressed on the cell surface of tumor cells (Dong et al., Nat Med 8:793-800, 2002).

In one aspect, this document features a method for treating a cancer patient. The method can include (a) identifying a cancer patient to be treated with a chemotherapeutic agent that causes DNA damage, (b) administering to the patient a molecule targeted to DNA-PKcs, wherein the molecule is administered in an amount sufficient to reduce the interaction of DNA-PKcs with B7-H1, and (c) administering the chemotherapeutic agent to the patient. The patient can be a human. The chemotherapeutic agent can be cisplatin, doxorubicin, SN38, paclitaxel, protein-bound paclitaxel, temozolomide, or carboplatin. The molecule targeted to DNA-PKcs can be NU7026, NU7441, IC86621, IC87102, IC87361, OK-1035, SU11752, vanillin, or IC486241, or can be an anti-DNA-PKcs antibody. The molecule targeted to DNA-PKcs and the chemotherapeutic agent can be administered simultaneously or sequentially.

In another aspect, this document features a method for treating a cancer patient, where the method can include (a) identifying the patient as having a tumor with cells that express B7-H1, and (b) administering to the patient a DNA-PKcs inhibitor and an anti-B7-H1 blocking antibody. The cancer patient can be a human. The cancer patient can be identified based on the level of B7-H1 protein in a sample obtained from the tumor, or based on the level of B7-H1 mRNA in a sample obtained from the tumor. The cancer can be a melanoma cancer, a breast cancer, a lung cancer, a renal cell carcinoma cancer, a pancreas cancer, a prostate cancer, a colon cancer, a brain cancer, a liver cancer, or an ovarian cancer. The DNA-PKcs inhibitor and the anti-B7-H1 blocking antibody can be administered to the cancer patient simultaneously or sequentially.

In another aspect, this document features a method for treating cancer, where the method can include administering a DNA-PKcs inhibitor and an anti-B7-H1 antibody to a mammal identified as having a tumor containing cells with an elevated level of B7-H1, where the DNA-PKcs inhibitor and the anti-B7-H1 antibody are administered under conditions in which the interaction of naturally-occurring B7-H1 with DNA-PKcs and the interaction of naturally-occurring B7-H1 with PD-1 or CD80 in the mammal is reduced after the administering. The mammal can be a human. The elevated level B7-H1 can be based on the level of B7-H1 protein in a sample obtained from the tumor, or based on the level of B7-H1 mRNA in a sample obtained from the tumor. The cancer can be a melanoma cancer, a breast cancer, a lung cancer, a renal cell carcinoma cancer, a pancreas cancer, a prostate cancer, a colon cancer, a brain cancer, a liver cancer, or an ovarian cancer. The DNA-PKcs inhibitor and the anti-B7-H1 blocking antibody can be administered to the mammal simultaneously or sequentially.

In still another aspect, this document features a composition containing a pharmaceutically acceptable carrier and a molecule targeted to DNA-PKcs for use in treating a cancer patient who also is to be treated with a chemotherapeutic agent that causes DNA damage, wherein the composition is to be administered in an amount sufficient to reduce the interaction of DNA-PKcs with B7-H1. The patient can be a human. The chemotherapeutic agent can be cisplatin, doxorubicin, SN38, paclitaxel, protein-bound paclitaxel, temozolomide, or carboplatin. The molecule targeted to DNA-PKcs can be NU7026, NU7441, IC86621, IC87102, IC87361, OK-1035, SU11752, vanillin, or IC486241, or can be an anti-DNA-PKcs antibody. The chemotherapeutic agent and the composition containing the molecule targeted to DNA-PKcs can be for simultaneous or sequential administration.

In another aspect, this document features a composition containing a pharmaceutically acceptable carrier and a DNA-PKcs inhibitor for use in treating cancer in a patient identified as having a tumor with cells that express B7-H1, wherein the patient also is to be treated with an anti-B7-H1 blocking antibody. The cancer patient can be a human. The cancer patient can be identified based on the level of B7-H1 protein in a sample obtained from the tumor, or based on the level of B7-H1 mRNA in a sample obtained from the tumor. The cancer can be a melanoma cancer, a breast cancer, a lung cancer, a renal cell carcinoma cancer, a pancreas cancer, a prostate cancer, a colon cancer, a brain cancer, a liver cancer, or an ovarian cancer. The anti-B7-H1 blocking antibody and the composition containing the DNA-PKcs inhibitor can be for simultaneous or sequential administration.

In still another aspect, this document features a composition containing a pharmaceutically acceptable carrier and a DNA-PKcs inhibitor for use in treating cancer in a mammal identified as having a tumor containing cells with an elevated level of B7-H1, wherein the mammal also is to be treated with an anti-B7-H1 antibody, and wherein the composition containing the DNA-PKcs inhibitor and the anti-B7-H1 antibody are to be administered under conditions in which the interaction of naturally-occurring B7-H1 with DNA-PKcs and the interaction of naturally-occurring B7-H1 with PD-1 or CD80 in the mammal are reduced after the administering. The mammal can be a human. The elevated level B7-H1 can be based on the level of B7-H1 protein in a sample obtained from the tumor, or based on the level of B7-H1 mRNA in a sample obtained from the tumor. The cancer can be a melanoma cancer, a breast cancer, a lung cancer, a renal cell carcinoma cancer, a pancreas cancer, a prostate cancer, a colon cancer, a brain cancer, a liver cancer, or an ovarian cancer. The anti-B7-H1 blocking antibody and the composition containing the DNA-PKcs inhibitor can be for simultaneous or sequential administration.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Although methods and materials similar or equivalent to those described herein can be used to practice the invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.

DESCRIPTION OF DRAWINGS

FIGS. 1A-1C demonstrate that B7-H1 confers tumor cell resistance to cytotoxic drugs. FIG. 1A is a series of graphs plotting relative survival of Mock/624mel (triangles) and B7-H1/624mel (squares) cells treated with the indicated drugs, as determined by MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) assay. The p-value for area under the curve (dose-response curves) was significant (p<0.01) for treatment with cisplatin (left), doxorubicin (center), and SN38 (right). One of three experiments is shown. Apoptosis of tumor cells treated with doxorubicin (1.5 ug/ml, 48 hr.) was analyzed by tetramethylrhodamine ethyl ester (TMRE) and Annexin V staining (FIG. 1 ), and by intracellular staining for active caspase-3 (FIG. 1C). Numbers are percentages of gated population.

FIGS. 2A-2C are pictures from co-immunoprecipitation and Western blotting (WB) experiments, demonstrating that B7-H1 associates with DNA-PKcs. FIG. 2A: Anti-B7-H1 Ab, but not control Ab, co-precipitated a protein band in B7-H1 transfected 624mel cells. FIG. 2B: Co-immunoprecipitation (IP) and Western blotting (WB) using cell lysate as input. FIG. 2C: Human primary T cells were activated by phytohemagglutinin (PHA) for 48 hours. B7-H1 was pulled down by anti-B7-H1 antibody but not control antibody. The association of B7-H1 with DNA-PKcs was detected by Western blotting using anti-DNA-PKcs antibody.

FIG. 3 is a graph plotting relative survival of tumor cells treated with a DNA-PKcs inhibitor, and showing that inhibition of DNA-PKcs reduced tumor drug resistance. Cells were pre-treated with DMSO or NU7026 (10 uM) for 1 hour before treatment with doxorubicin (Dox). The relative survival of tumor cells was measured by MTS assay 72 hours after Dox treatment.

FIG. 4 is a diagram showing potential molecular mechanisms for B7-H1-mediated tumor chemoresistance.

FIG. 5A is a cross-species alignment of the B7-H1 intracellular domains (ICD) from human (SEQ ID NO:1), chimpanzee (SEQ ID NO:1), Rhesus monkey (SEQ ID NO:2), marmoset (SEQ ID NO:3), sooty mangabey (SEQ ID NO:4), cow (SEQ ID NO:5), pig (SEQ ID NO:6), mouse (SEQ ID NO:7), and rat (SEQ ID NO:8). Conserved residues are in red. FIG. 5B is a diagram of Flag-B7-H1 ICD domain fragments (SEQ ID NOS:9-13).

FIG. 6 is a series of pictures showing co-localization of B7-H1 and DNA-PKcs. A human breast tumor cell line (MDA-MB-231) was treated with doxorubicin (2 ug/ml) for 2 hours. Co-localization of B7-H1 and DNA-PKcs was observed in the nuclei. Arrows or arrowheads indicate B7-H1 in plasma or in nuclei, respectively.

FIG. 7 is a picture of a blot showing B7-H1 or control (GAPDH) expression in human tumor cells (MDA-MB-231) following transfection with control or B7-H1 shRNA.

FIGS. 8A-8C demonstrate that B7-H1 enhances activation of the MAPK/ERK pathway. FIG. 8A is a picture (top) and a graph (bottom) showing the results of an antibody array assay of phosphorylation of molecules in the MAPK/ERK pathway. The levels of phospho-ERK and total ERK were analyzed by Western blotting (FIG. 8B) and flow cytometry (FIG. 8C). Numbers are mean fluorescence intensity (MFI).

FIG. 9 is a series of graphs plotting the levels of phosphorylated ERK (top graphs) and total ERK (bottom graphs) in Mock/624mel (left) and B7-H1/624mel (right) tumor cells treated with DMSO or NU7026. Cells were treated with DMSO or NU7026 (10 uM) for 24 hours before intracellular staining for phospho-ERK or total ERK. Numbers are MFI. Inhibition of DNA-PKcs reduced ERK activation, as indicated in the diagram on the right.

FIG. 10 is a schematic showing a potential DNA-PKcs/ERK/Bim pathway that may be used by B7-H1 to counter tumor cell apoptosis.

FIG. 11 is a schematic showing a potential DNA-PKcs/Akt/Bad pathway that may be used by B7-H1 to counter tumor cell apoptosis.

FIG. 12 contains representative nucleic acid (top) and amino acid (bottom) sequences for human B7-H1 (SEQ ID NOS:14 and 15, respectively).

FIG. 13 contains representative nucleic acid (top) and amino acid (bottom) sequences for human PD-1 (SEQ ID NOS:16 and 17, respectively).

FIGS. 14A and 14B contain representative nucleic acid (14A) and amino acid (14B) sequences for human CD80 (SEQ ID NOS:18 and 19, respectively).

FIGS. 15A and 15B show that DNA-PKcs activity is required for the association of DNA-PKcs with B7-H1. MBA-MD-231 human breast cancer cells, which are positive for B7-H1, were incubated with NU7026, an inhibitor of DNA-PKCs. FIG. 15A shows an immuno-precipitation assay, demonstrating that NU7026 abolished the association of B7-H1 with DNA-PKcs. FIG. 15B is a series of pictures from an immunofluorescence assay in which the cells treated with doxorubicin, NU7026, or both, and stained for DNA-PKcs, DNA, or B7-H1. Doxorubicin-induced co-localization (arrow, upper right panel) of B7-H1 and DNA-PKcs at the nucleus was blocked by NU7026 (lower right panel).

DETAILED DESCRIPTION

This document provides methods and materials for treating cancer in patients with tumors that are chemoresistant or are at risk of becoming chemoresistant. For example, this document provides methods and materials for identifying a cancer patient (e.g., a mammal such as a human, non-human primate, cow, sheep, pig, dog, rabbit, rat, or mouse) as having a tumor that expresses B7-H1 at an elevated level, and treating the patient with a molecule that can interfere with the interaction between B7-H1 and DNA-PKcs. In some embodiments, the methods provided herein also can include treating the patient with a molecule that can interfere with the interaction between B7-H1 and PD-1, and/or the interaction between B7-H1 and CD80 (e.g., an antibody against B7-H1, PD-1, or CD80, or a fusion protein containing a portion of PD-1 or a portion of CD80 fused to an immunoglobulin (Ig) Fc domain).

The term “elevated level” as used herein with respect to a level of B7-H1 refers to a level that is greater (e.g., 50% greater, 2-fold greater, 3-fold greater, or more than 3-fold greater) than a reference level of B7-H1. The term “reference level” as used herein with respect to B7-H1 can refer to the level of B7-H1 typically observed in cells from healthy subjects without cancer. In some embodiments, for example, a reference level of B7-H1 can be the average level of B7-H1 present in samples obtained from a random sampling of 50 humans free of cancer. In some embodiments, B7-H1 levels can be determined based on cell staining, and “elevated” and “reference” levels can set based on the percentage of evaluated cells that stain positive for B7-H1. For example, in some embodiments, samples (e.g., tumor samples) in which five percent or less (e.g., five percent, four percent, three percent, two percent, one percent, or less than one percent) of the cells stain positive for B7-H1 can be considered B7-H1 negative. In some embodiments, samples (e.g., tumor samples) in which ten percent or more (e.g., ten percent, 20 percent, 25 percent, 30 percent, 40 percent, 50 percent, or more than 50 percent) of the cells stain positive for B7-H1 can be considered to have elevated levels of B7-H1 expression.

The presence of an elevated level of B7-H1 can be determined by measuring, for example, B7-H1 protein levels or B7-H1 nucleic acid levels. For example, the level of B7-H1 protein can be measured in a tumor sample from a mammal with cancer using cell staining, western blotting, or other immunological techniques. The level of B7-H1 expression also can be measured at the nucleic acid level, using Northern blotting, or any other method suitable for determining mRNA levels of CD274, which encodes the B7-H1 protein. In some cases, B7-H1 protein or nucleic acid levels can be measured in ascites samples, or lymphoid organ samples. It will be appreciated that levels from comparable samples are used when determining whether or not a particular level is an elevated level.

A representative example of a human B7-H1 nucleic acid has the sequence set forth in GENBANK® Accession No. AF177937 (GI No. 6708118) (SEQ ID NO:14; FIG. 12 ), and a representative human B7-H1 polypeptide has the sequence set forth in GENBANK® Accession No. AAF25807 (GI No. 6708119) (SEQ ID NO:15; FIG. 12 ).

A representative example of a human PD-1 nucleic acid can have the sequence set forth in GENBANK® Accession No. BC074740.2 (GI No. 50960296) (SEQ ID NO:16; FIG. 13 ), and representative example of a human PD-1 polypeptide has the sequence set forth in GENBANK® Accession No. AAH74740.1 (GI No. 49902307) (SEQ ID NO:17; FIG. 13 ).

A representative example of a human CD80 nucleic acid has the sequence set forth in NCBI Reference No. NM_005191.3 (GI No. 113722122) (SEQ ID NO:18; FIG. 14A), and a representative example of a human CD80 polypeptide has the sequence set forth in NCBI Reference No. NP_005182.1 (GI No. 4885123) (SEQ ID NO:19; FIG. 14B).

After the level of B7-H1 within a tumor sample from a mammal is determined, the level can be compared to a reference level, and the mammal can be classified as having or not having an elevated level of B7-H1. If the mammal is identified as having an elevated level of B7-H1, the mammal can be treated with a first molecule that inhibits the interaction between B7-H1 and DNA-PKcs. For example, a small molecule DNA-PKcs inhibitor such as NU7026, NU7441, IC86621, IC87102, IC87361, OK-1035, SU11752, vanillin, or IC486241 can be administered to the mammal. For the structures of these molecules, see, e.g., Davidson et al., Front Pharmacol 4:1-7, 2013. In some embodiments, an anti-DNA-PKcs antibody can be administered to block the interaction between B7-H1 and DNA-PKcs. Further, B7-H1 peptides can be useful. Such peptides can be fragments of B7-H1 (e.g., fragments containing about 10-20, about 20-50, or about 50-100 amino acids) that include the DNA-PKcs binding domain, such that they can inhibit the interaction between B7-H1 and DNA-PKcs. Such peptides can be referred to as “interfering B7-H1 small peptides.”

In some embodiments, the mammal also can be treated with a second molecule that inhibits the interaction between B7-H1 and PD-1 and/or the interaction between B7-H1 and CD80. Examples of such second molecules include, without limitation, antibodies (e.g., anti-B7-H1 antibodies, anti-PD-1 antibodies, or anti-CD80 antibodies), and fusion proteins (e.g., PD-1 fusion proteins or CD80 fusion proteins). Such fusion proteins can contain, for example, the extracellular domain of PD-1 fused to an IgG Fc domain, or the extracellular domain of CD80 fused to an IgG Fc domain. Binding of the fusion proteins to B7-H1 can reduce or block the ability of B7-H1 to interact with PD-1 and/or CD80.

The term “antibody” includes monoclonal antibodies, polyclonal antibodies, recombinant antibodies, humanized antibodies (Jones et al. (1986) Nature 321:522-525; Riechmann et al. (1988) Nature 332:323-329; and Presta (1992) Curr. Op. Struct. Biol. 2:593-596), chimeric antibodies (Morrison et al. (1984) Proc. Natl. Acad. Sci. USA 81:6851-6855), multispecific antibodies (e.g., bispecific antibodies) formed from at least two antibodies, and antibody fragments. The term “antibody fragment” comprises any portion of the afore-mentioned antibodies, such as their antigen binding or variable regions. Examples of antibody fragments include Fab fragments, Fab′ fragments, F(ab′)2 fragments, Fv fragments, diabodies (Hollinger et al. (1993) Proc. Natl. Acad. Sci. USA 90:6444-6448), single chain antibody molecules (Plückthun in: The Pharmacology of Monoclonal Antibodies 113, Rosenburg and Moore, eds., Springer Verlag, N.Y. (1994), 269-315) and other fragments as long as they exhibit the desired capability of binding to their target (e.g., B7-H1, PD-1, or CD80).

Examples of anti-human B7-H1 antibodies include, without limitation, anti-human B7-H1 antibodies commercially available from Biolegend (e.g., Catalog No. 329701 or 329702; San Diego, Calif.) or eBioscience (e.g., Catalog No. 14-5983-80 or 14-5983-82).

Examples of anti-human PD-1 antibodies include, without limitation, anti-human PD-1 antibodies commercially available from Biolegend (e.g., Catalog No. 329904 or 329905) or eBioscience (Catalog No. 12-2799-42; San Diego, Calif.).

Examples of anti-human CD80 antibodies include, without limitation, anti-human CD8 antibodies commercially available from Biolegend (e.g., Catalog No. 305201 or 305202) or eBioscience (e.g., Catalog No. 14-0809-80 or 14-0809-82).

The term “antibody,” as used herein, also includes antibody-like molecules that contain engineered sub-domains of antibodies or naturally occurring antibody variants. These antibody-like molecules may be single-domain antibodies such as VH-only or VL-only domains derived either from natural sources such as camelids (Muyldermans et al. (2001) Rev. Mol. Biotechnol. 74:277-302) or through in vitro display of libraries from humans, camelids or other species (Holt et al. (2003) Trends Biotechnol. 21:484-90). In certain embodiments, the polypeptide structure of the antigen binding proteins can be based on antibodies, including, but not limited to, minibodies, synthetic antibodies (sometimes referred to as “antibody mimetics”), human antibodies, antibody fusions (sometimes referred to as “antibody conjugates”), and fragments thereof, respectively.

An “Fv fragment” is the minimum antibody fragment that contains a complete antigen-recognition and -binding site. This region consists of a dimer of one heavy chain variable domain and one light chain variable domain in tight, non-covalent association. It is in this configuration that the three CDR's of each variable domain interact to define an antigen-binding site on the surface of the VH-VL dimer. Collectively, the six CDR's confer antigen-binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three CDR's specific for an antigen) has the ability to recognize and bind the antigen, although usually at a lower affinity than the entire binding site. The “Fab fragment” also contains the constant domain of the light chain and the first constant domain (CHI) of the heavy chain. The “Fab fragment” differs from the “Fab′ fragment” by the addition of a few residues at the carboxy terminus of the heavy chain C_(H)1 domain, including one or more cysteines from the antibody hinge region. The “F(ab′)2 fragment” originally is produced as a pair of “Fab′ fragments” which have hinge cysteines between them. Methods of preparing such antibody fragments, such as papain or pepsin digestion, are known to those skilled in the art.

An antibody can be of the IgA-, IgD-, IgE, IgG- or IgM-type, including IgG- or IgM-types such as, without limitation, IgG1-, IgG2-, IgG3-, IgG4-, IgM1- and IgM2-types. For example, in some cases, an antibody can be of the IgG1-, IgG2- or IgG4-type.

In some embodiments, antibodies as used in the methods described herein can be fully human or humanized antibodies. Human antibodies can avoid certain problems associated with xenogeneic antibodies, such as antibodies that possess murine or rat variable and/or constant regions. First, because the effector portion is human, it can interact better with other parts of the human immune system, e.g., to destroy target cells more efficiently by complement-dependent cytotoxicity or antibody-dependent cellular cytotoxicity. Second, the human immune system should not recognize the antibody as foreign. Third, the half-life in human circulation will be similar to naturally occurring human antibodies, allowing smaller and less frequent doses to be given. Methods for preparing human antibodies are known in the art.

In addition to human antibodies, “humanized” antibodies can be used, and can have many advantages. Humanized antibodies generally are chimeric or mutant monoclonal antibodies from mouse, rat, hamster, rabbit or other species, bearing human constant and/or variable region domains or specific changes. Techniques for generating humanized antibodies are well known to those of skill in the art. For example, controlled rearrangement of antibody domains joined through protein disulfide bonds to form new, artificial protein molecules or “chimeric” antibodies can be utilized (Konieczny et al. (1981) Haematologia (Budap.) 14:95). Recombinant DNA technology can be used to construct gene fusions between DNA sequences encoding mouse antibody variable light and heavy chain domains and human antibody light and heavy chain constant domains (Morrison et al. (1984) Proc. Natl. Acad. Sci. USA 81:6851).

DNA sequences encoding antigen binding portions or complementarity determining regions (CDR's) of murine monoclonal antibodies can be grafted by molecular means into DNA sequences encoding frameworks of human antibody heavy and light chains (Jones et al. (1986) Nature 321:522; Riechmann et al. (1988) Nature 332:323). Expressed recombinant products are called “reshaped” or humanized antibodies, and comprise the framework of a human antibody light or heavy chain and antigen recognition portions, CDR's, of a murine monoclonal antibody.

Other methods for designing heavy and light chains and for producing humanized antibodies are described in, for example, U.S. Pat. Nos. 5,530,101; 5,565,332; 5,585,089; 5,639,641; 5,693,761; 5,693,762; and 5,733,743. Yet additional methods for humanizing antibodies are described in U.S. Pat. Nos. 4,816,567; 4,935,496; 5,502,167; 5,558,864; 5,693,493; 5,698,417; 5,705,154; 5,750,078; and 5,770,403, for example.

Molecules that interfere with the interaction between B7-H1 and DNA-PKcs, the interaction between B7-H1 and PD-1, and/or the interaction between B7-H1 and CD80, as described herein (e.g., small molecule inhibitors of DNA-PKcs, antibodies against B7-H1, DNA-PKcs, PD-1, and CD80, and fusion proteins containing portions of PD-1 or CD80 linked to an Ig Fc domain), can be incorporated into pharmaceutical compositions for treatment of cancer. Thus, this document also provides the use of such molecules in the manufacture of medicaments for treating cancer. The compositions further can include one or more pharmaceutically acceptable carriers, diluents and/or adjuvants.

A “pharmaceutically acceptable carrier” (also referred to as an “excipient” or a “carrier”) is a pharmaceutically acceptable solvent, suspending agent, stabilizing agent, or any other pharmacologically inert vehicle for delivering one or more therapeutic compounds to a subject, which is nontoxic to the cell or mammal being exposed thereto at the dosages and concentrations employed. Pharmaceutically acceptable carriers can be liquid or solid, and can be selected with the planned manner of administration in mind so as to provide for the desired bulk, consistency, and other pertinent transport and chemical properties, when combined with one or more of therapeutic compounds and any other components of a given pharmaceutical composition. Typical pharmaceutically acceptable carriers include, by way of example and not limitation: water, saline solution, binding agents (e.g., polyvinylpyrrolidone or hydroxypropyl methylcellulose), fillers (e.g., lactose and other sugars, gelatin, or calcium sulfate), lubricants (e.g., starch, polyethylene glycol, or sodium acetate), disintegrates (e.g., starch or sodium starch glycolate), and wetting agents (e.g., sodium lauryl sulfate). Pharmaceutically acceptable carriers also include aqueous pH buffered solutions or liposomes (small vesicles composed of various types of lipids, phospholipids and/or surfactants which are useful for delivery of a drug to a mammal). Further examples of pharmaceutically acceptable carriers include buffers such as phosphate, citrate, and other organic acids, antioxidants such as ascorbic acid, low molecular weight (less than about ten residues) polypeptides, proteins such as serum albumin, gelatin, or immunoglobulins, hydrophilic polymers such as polyvinylpyrrolidone, amino acids such as glycine, glutamine, asparagine, arginine or lysine, monosaccharides, disaccharides, and other carbohydrates including glucose, mannose or dextrins, chelating agents such as EDTA, sugar alcohols such as mannitol or sorbitol, salt-forming counterions such as sodium, and/or nonionic surfactants such as TWEEN™, polyethylene glycol (PEG), and PLURONICS™.

Pharmaceutical compositions can be formulated by mixing one or more active agents (e.g., a DNA-PKcs inhibitor or an anti-B7-H1 blocking antibody) with one or more physiologically acceptable carriers, diluents, and/or adjuvants, and optionally other agents that are usually incorporated into formulations to provide improved transfer, delivery, tolerance, and the like. Pharmaceutical compositions can be formulated, e.g., in lyophilized formulations, aqueous solutions, dispersions, or solid preparations, such as tablets, dragees or capsules. A multitude of appropriate formulations can be found in the formulary known to pharmaceutical chemists: Remington's Pharmaceutical Sciences (18th ed, Mack Publishing Company, Easton, Pa. (1990)), particularly Chapter 87 by Block, Lawrence, therein. These formulations include, for example, powders, pastes, ointments, jellies, waxes, oils, lipids, lipid (cationic or anionic) containing vesicles (such as LIPOFECTIN™), DNA conjugates, anhydrous absorption pastes, oil-in-water and water-in-oil emulsions, emulsions carbowax (polyethylene glycols of various molecular weights), semi-solid gels, and semi-solid mixtures containing carbowax. Any of the foregoing mixtures may be appropriate in treatments and therapies as described herein, provided that the active agent in the formulation is not inactivated by the formulation and the formulation is physiologically compatible and tolerable with the route of administration. See, also, Baldrick (2000) Regul. Toxicol. Pharmacol. 32:210-218; Wang (2000) Int. J Pharm. 203:1-60; Charman (2000) J. Pharm. Sci. 89:967-978; and Powell et al. (1998) PDA J. Pharm. Sci. Technol. 52:238-311), and the citations therein for additional information related to formulations, excipients and carriers well known to pharmaceutical chemists.

Pharmaceutical compositions include, without limitation, solutions, emulsions, aqueous suspensions, and liposome-containing formulations. These compositions can be generated from a variety of components that include, for example, preformed liquids, self-emulsifying solids and self-emulsifying semisolids. Emulsions are often biphasic systems comprising of two immiscible liquid phases intimately mixed and dispersed with each other; in general, emulsions are either of the water-in-oil (w/o) or oil-in-water (o/w) variety. Emulsion formulations have been widely used for oral delivery of therapeutics due to their ease of formulation and efficacy of solubilization, absorption, and bioavailability.

Compositions and formulations can include sterile aqueous solutions, which also can contain buffers, diluents and other suitable additives (e.g., penetration enhancers, carrier compounds and other pharmaceutically acceptable carriers). Compositions additionally can contain other adjunct components conventionally found in pharmaceutical compositions. Thus, the compositions also can include compatible, pharmaceutically active materials such as, for example, antipruritics, astringents, local anesthetics or anti-inflammatory agents, or additional materials useful in physically formulating various dosage forms of the compositions provided herein, such as dyes, flavoring agents, preservatives, antioxidants, opacifiers, thickening agents and stabilizers. Furthermore, the composition can be mixed with auxiliary agents, e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, colorings, flavorings, and aromatic substances. When added, however, such materials should not unduly interfere with the biological activities of the polypeptide components within the compositions provided herein. The formulations can be sterilized if desired.

In some embodiments, a composition containing a DNA-PKcs inhibitor and/or an antibody or fusion protein as provided herein (e.g., an anti-B7-H7, anti-DNA-PKcs, anti-PD-1, or anti-CD80 antibody, or a PD-1-Fc or CD80-Fc fusion protein) can be in the form of a solution or powder with or without a diluent to make an injectable suspension. The composition may contain additional ingredients including, without limitation, pharmaceutically acceptable vehicles, such as saline, water, lactic acid, mannitol, or combinations thereof, for example.

Methods for using an agent (e.g., a small molecule inhibitor of DNA-PKcs, an antibody against B7-H1, DNA-PKcs, PD-1, or CD80, or a PD-1-Fc or CD80-Fc fusion protein) or a composition containing such an agent to treat cancer patients also are provided herein. The methods can include, for example, administering an agent or composition to a subject identified as being in need thereof. In some embodiments, a method as provided herein can further include steps such as identifying a mammal (e.g., a human cancer patient) that is to be treated with a chemotherapeutic agent (e.g., cisplatin, doxorubicin, SN38, paclitaxel, protein-bound paclitaxel (e.g., ABRAXANE®), temozolomide (e.g., TEMODAR®), or carboplatin) that causes DNA damage, or identifying a mammal as having a tumor with cells that express B7-H1. For example, a method can include identifying a mammal to be treated with a chemotherapeutic agent that causes DNA damage, and treating the mammal with an agent that inhibits the interaction between B7-H1 and DNA-PKcs. In some cases, a method can further include the step of administering the chemotherapeutic agent that causes DNA damage.

Any appropriate method can be used to administer a molecule as described herein to a mammal. Administration can be, for example, parenteral (e.g., by subcutaneous, intrathecal, intraventricular, intramuscular, or intraperitoneal injection, or by intravenous drip). Administration can be rapid (e.g., by injection) or can occur over a period of time (e.g., by slow infusion or administration of slow release formulations). In some embodiments, administration can be topical (e.g., transdermal, sublingual, ophthalmic, or intranasal), pulmonary (e.g., by inhalation or insufflation of powders or aerosols), or oral. In addition, a composition containing an antibody or fusion protein as described herein can be administered prior to, after, or in lieu of surgical resection of a tumor.

Compositions containing an antibody (e.g., an anti-B7-H1 antibody, an anti-DNA-PKcs antibody, an anti-PD-1 antibody, or an anti-CD80 antibody), a small molecule (e.g., NU7026) or a fusion protein (e.g., a PD-1-Fc fusion or a CD80-Fc fusion) can be administered to a mammal in any appropriate amount, at any appropriate frequency, and for any appropriate duration effective to achieve a desired outcome (e.g., to increase progression-free survival, or to reduce progression of the cancer). Combination therapies, in which a DNA-PKcs inhibitor and an anti-B7-H1 blocking antibody are administered to a mammal, can be particularly useful, as such therapies can target both chemoresistance and immunoresistance. For example, a first composition containing a DNA-PKcs inhibitor and a second composition containing an anti-B7-H1 antibody can be administered, either simultaneously (e.g., via simultaneous administration of separate compositions, or via administration of a composition containing both agents), or sequentially.

In some embodiments, a DNA-PKcs inhibitor and an anti-B7-H1 antibody can be administered to a mammal having cancer to reduce the progression rate of the cancer by 5, 10, 25, 50, 75, 100, or more percent. For example, the progression rate can be reduced such that no additional cancer progression is detected. In some embodiments, a DNA-PKcs inhibitor and an anti B7-H1 antibody can be administered to a mammal having cancer under conditions where progression-free survival is increased (e.g., by 5, 10, 25, 50, 75, 100, or more percent) as compared to the median progression-free survival of corresponding mammals having untreated cancer or the median progression-free survival of corresponding mammals having cancer and treated with other therapies (e.g., immune or chemotherapeutic agents alone). Progression-free survival can be measured over any length of time (e.g., one month, two months, three months, four months, five months, six months, or longer). Any appropriate method can be used to determine whether or not the progression rate of cancer is reduced. For skin cancer (e.g., melanoma), for example, the progression rate can be assessed by imaging tissue at different time points and determining the amount of cancer cells present. The amounts of cancer cells determined within tissue at different times can be compared to determine the progression rate. After treatment as described herein, the progression rate can be determined again over another time interval. In some cases, the stage of cancer after treatment can be determined and compared to the stage before treatment to determine whether or not the progression rate has been reduced.

An effective amount of a composition containing an antibody as provided herein can be any amount that reduces a symptom of the condition being treated, without significant toxicity. With cancer, for example, an effective amount can reduce the progression rate of the cancer, increase the progression-free survival rate, or increase the median time to progression. Optimum dosages can vary depending on the relative potency of individual polypeptides (e.g., antibodies and fusion proteins), and can generally be estimated based on EC₅₀ found to be effective in in vitro and in vivo animal models. Typically, dosage is from 0.01 μg to 100 g per kg of body weight. For example, an effective amount of an antibody or fusion protein can be from about 1 mg/kg to about 100 mg/kg (e.g., about 5 mg/kg, about 10 mg/kg, about 20 mg/kg, about 50 mg/kg, or about 75 mg/kg). If a particular subject fails to respond to a particular amount, then the amount of the antibody can be increased by, for example, two fold. After receiving this higher concentration, the subject can be monitored for both responsiveness to the treatment and toxicity symptoms, and adjustments made accordingly. The effective amount can remain constant or can be adjusted as a sliding scale or variable dose depending on the mammal's response to treatment. Various factors can influence the actual effective amount used for a particular application. For example, the frequency of administration, duration of treatment, use of multiple treatment agents, route of administration, and severity of the clinical condition may require an increase or decrease in the actual effective amount administered.

The frequency of administration can be any frequency that reduces the progression rate of cancer, increases the progression-free survival rate, or increases the median time to progression without producing significant toxicity to the mammal. For example, the frequency of administration can be once or more daily, biweekly, weekly, monthly, or even less. The frequency of administration can remain constant or can be variable during the duration of treatment. A course of treatment can include rest periods. For example, a composition containing one or more agents (e.g., a small molecule, antibody, or fusion protein as provided herein) can be administered over a two week period followed by a two week rest period, and such a regimen can be repeated multiple times. As with the effective amount, various factors can influence the actual frequency of administration used for a particular application. For example, the effective amount, duration of treatment, use of multiple treatment agents, route of administration, and severity of the cancer may require an increase or decrease in administration frequency.

An effective duration for administering a composition provided herein can be any duration that reduces the progression rate of cancer, increases the progression-free survival rate, or increases the median time to progression without producing significant toxicity to the mammal. Thus, the effective duration can vary from several days to several weeks, months, or years. In general, the effective duration for the treatment of cancer can range in duration from several weeks to several months. In some cases, an effective duration can be for as long as an individual mammal is alive. Multiple factors can influence the actual effective duration used for a particular treatment. For example, an effective duration can vary with the frequency of administration, effective amount, use of multiple treatment agents, route of administration, and severity of the cancer.

After administering one or more agents as provided herein to a mammal, the mammal can be monitored to determine whether or not the treatment was effective. For example, a mammal can be assessed after treatment to determine whether or not the progression rate of the cancer has been reduced. Any method, including those that are standard in the art, can be used to assess progression and survival rates.

The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims.

EXAMPLES Example 1—B7-H1 Renders Tumor Cells Resistant to Drugs that Cause DNA Damage

Experiments were conducted to test whether B7-H1-expressing tumors would show resistance to drugs that cause DNA damage. Along with cisplatin, which crosslinks DNA, doxorubicin (a topoisomerase II inhibitor that leads to generation of free radicals) and SN38 (a topoisomerase I inhibitor) were tested. Drug sensitivity in B7-H1- and Mock-transfected 624mel melanoma cells was examined in cultures with varying concentrations of the drugs. After 72 hours of culture, tumor cell survival was measured with a MTS assay (Pei et al., Cancer Cell 16:259-266, 2009). As shown in FIG. 1A, B7-H1/624mel cells were more resistant than Mock/624mel cells to cisplatin, doxorubicin, and SN38. Consistent with a previous pharmacogenetic analysis, these data supported the idea that B7-H1 renders tumor cells resistant to cytotoxic chemotherapeutic agents. Since a mechanism of action of most cytotoxic drugs is to induce apoptosis (Sedletska et al., Curr Med Chem Anti-cancer Agents 5:251-265, 2005; and Wang et al., J Biol Chem 279:25535-25543, 2004), apoptosis of B7-H1/624mel and Mock/624mel tumor cells was measured and compared after treatment with doxorubicin. Specifically, apoptosis was measured based on the binding of Annexin V (AV) and the levels of tetramethylrhodamine ethyl ester (TMRE), a marker for mitochondria membrane potential (Jayaraman, J Immunolog Meth 306:68-79, 2005). As shown in FIG. 1B, B7-H1/624mel cells had 5-fold less apoptosis compared to Mock/624mel cells following treatment with doxorubicin. The level of active caspase-3 (an executive molecule of apoptosis) also was lower in B7-H1/624mel cells compared with Mock/624mel cells (FIG. 1C). Thus, B7-H1 may render tumor cells resistant to cytotoxic drugs by reducing their apoptotic potential to cytotoxic condition.

Example 2—B7-H1 is Associated with DNA-PKcs

A co-immunoprecipitation (Co-IP) assay with tumor cell lysates using anti-B7-H1 monoclonal antibody resulted in identification of a 450-kDa protein band (FIG. 2A). The protein band identified was larger than and distinct from the membrane proteins PD-1 (55 kDa) and CD80 (65 kDa) that also have been reported to interact with B7-H1. The band was excised from the gel, and mass spectroscopy revealed that the major component was DNA-PKcs (DNA dependent protein kinase, catalytic subunit). To confirm the association of B7-H1 with DNA-PKcs, Co-IP assays were performed using anti-DNA-PKcs and anti-B7-H1 monoclonal antibodies in a tumor cell line that constitutively expresses B7-H1 (Karpas299) and in a B7-H1-transfected tumor cell line (B7-H1/624mel). Both DNA-PKcs and B7-H1 were pulled down by their respective antibodies in B7-H1 transfected 624mel cells, as well as in the endogenous B7-H1-positive Karpas299 cells (FIG. 2B), suggesting that DNA-PKcs and B7-H1 indeed associate in vivo. Significantly, an association of DNA-PKcs and B7-H1 was detected in activated (known to up-regulate B7-H1 expression) but not resting human primary T cells (FIG. 2C), suggesting the association of B7-H1 with DNA-PKcs may be a general biological interaction that is not limited to tumor cells.

Example 3—Inhibition of DNA-PKcs Activity Abolishes B7-H1-Mediated Chemoresistance

To test whether the association of B7-H1 with DNA-PKcs is a mechanism of drug resistance, the effects of NU7026 on drug sensitivity of B7-H1- or Mock-transfected 624mel cells were tested. NU7026 is an ATP-competitive DNA-PKcs inhibitor, and 10 uM NU7026 completely inhibits DNA-PKcs activity (Veuger et al., Cancer Res 63:6008-6015, 2003; and Willmore et al., Blood 103:4659-4665, 2004). Using the same dose (10 uM) of NU7026, experiments were conducted to determine whether NU7026 would affect the drug sensitivity of B7-H1/624mel cells. As shown in FIG. 3 , B7-H1/624mel cells demonstrated resistance to doxorubicin, compared with Mock/624mel cells. After pretreatment with NU7026, however, B7-H1/624mel cells lost their resistance to doxorubicin and had comparable drug sensitivity with Mock/624mel cells, suggesting that DNA-PKcs may contribute to B7-H1-mediated drug resistance (FIG. 3 ). NU7026 also increased the drug sensitivity of Mock/624mel cells, suggesting DNA-PKcs may be a downstream element of B7-H1 signaling pathway.

Taken together, these preliminary data strongly suggest that DNA-PKcs plays a key role in B7-H1-mediated tumor chemoresistance, and that B7-H1 is a DNA damage checkpoint molecule that, association with DNA-PKcs, promotes tumor survival via DNA damage repair and activation of pro-survival signaling pathways, thus countering cytotoxic effects of chemotherapeutic agents (FIG. 4 ). To test this hypothesis, experiments are conducted to (1) define the role of B7-H1 interaction with DNA-PKcs in DNA damage repair and (2) define the role of B7-H1 interaction with DNA-PKcs in the activation of pro-survival signaling pathways. Conceptually, these studies extend the role of B7-H1, originally defined as an immune checkpoint molecule, to a DNA damage checkpoint molecule of tumor cells upon treatment with cytotoxic drugs.

Example 4—Identifying the Binding Sites(s) of B7-H1 in Association with DNA-PKcs

The anti-apoptosis function of B7-H1 has been identified in its intracellular domain (ICD) in tumor cells (Azuma et al., Blood 111:3635-3643, 2008). It is possible that B7-H1 uses its ICD in association with DNA-PKcs to achieve its anti-apoptosis function in tumor cells. The B7-H1 ICD has eight amino acid residues that are conserved across species (FIG. 5A, red font). Based on their distribution and locations, these amino acids can be grouped in three regions (I, II, and III).

To test which region is required for B7-H1 to associate with DNA-PKcs, individual region deletions or truncations are made for the B7-H1 ICD, as shown in FIG. 5B. Next, single residue mutations of each conserved amino acid in the required region are generated to test which amino acid is required for binding. Candidate amino acids are changed to Ala in this mutagenesis assay. Flag-B7-H1 ICD fusion proteins carrying regional truncations or individual mutations are produced. B7-H1-negative 624mel tumor cells are transfected with Flag-B7-H1 ICD, and are used in Co-IP (using anti-Flag antibody in pull-down assays) to assess the association of mutant or truncated B7-H1 ICD with DNA-PKcs. It is noted that the transmembrane domain of B7-H1 may be needed if the association with DNA-PKcs requires anchoring of B7-H1 to the cytoplasm or nuclear membrane. In this case, the transmembrane domain of B7-H1 is included in the Flag-B7-H1 fusion protein for the Co-IP assay.

Example 5—Identifying the Effects of B7-H1 on DNA Repair Function of DNA-PKcs

B7-H1 undergoes redistribution from the cell surface into the nucleus in human breast tumor cells upon treatment with the cytotoxic drug, doxorubicin (Ghebeh et al., supra). Using the same model (MDA-MB-231, B7-H1 positive cell line), studies were conducted to examine whether translocation of B7-H1 results in close association with DNA-PKcs in the nucleus following drug treatment. The results shown in FIG. 6 demonstrate that before treatment with cytotoxic drug, DNA-PKcs was mainly localized in nuclei and B7-H1 was mainly localized in cytoplasm of tumor cells (arrows). After treatment, B7-H1 was enriched in the nuclei, and co-localization of B7-H1 and DNA-PKcs was observed in the nuclei (arrow heads in FIG. 6 ), suggesting that B7-H1 may be recruited to the nucleus to regulate DNA-PKcs activity in responses to DNA damage caused by chemotherapeutic drugs.

The phosphorylation of DNA-PKcs is required for rejoining of DNA double-strand breaks (DSBs) (Chan et al., Genes Dev 16:2333-2338, 2002), raising the possibility that B7-H1 stimulates DNA-PKcs activity to repair DNA DSBs. To test this, gamma-H2AX (γH2AX) is used. γH2AX has been widely used as a sensitive marker for DSBs (Banath et al., BMC Cancer 10:4, 2010; Mah et al., Leukemia 24:679-686, 2010; and Yuan et al., FEBS Lett 584:3717-3724, 2010). Nuclear yH2AX is measured by anti-phospho-H2AX (Ser139) (Cell Signaling, clone 20E3) in confocal immunofluorescence (IF) assays. A time course examination is conducted, with comparison of the distribution (nuclear foci or nuclear periphery) of γH2AX between B7-H1 positive and B7-H1 negative (knockdown) tumor cells upon treatment with cytotoxic drug (doxorubicin or cisplatin). As shown in FIG. 7 , a method to knockdown B7-H1 in human tumor cells has been established. Five different fields are scored for γH2AX distribution and expression. Fisher's exact test is used to calculate the p-value. To quantify γH2AX expression and its relation with a specific cell cycle phase, a flow cytometry-based assay is used to measure the nuclear levels of γH2AX (Kataoka et al., J Rad Res 47:245-257, 2006) while measuring DNA content with propidium iodide (Solier et al., Mol Cell Biol 29:68-82, 2009).

To measure DNA-PKcs activity, anti-phospho-DNA-PKcs (Thr2609) antibody is used (BioLegend, clone 10B1) to detect auto-phosphorylated DNA-PKcs by Western blotting following treatment with cytotoxic agents over a course of time. To directly measure the DNA repair function of DNA-PKcs, an EJ5GFP-based chromosomal break reporter (from the Addgene plasmid repository) is used to measure DNA-PKcs mediated non-homologous end joining (NHEJ; Bennardo et al., PLoS Genet 4:e1000110, 2008; and Gunn et al., J Biol Chem 286:42470-42482, 2011). EJ5GFP contains a promoter that is separated from a GFP coding cassette by a puro gene that is flanked by two I-SceI sites that are in the same orientation. Once the puro gene is excised by NHEJ repair of the two I-SceI-induced DSBs, the promoter is joined to the rest of the expression cassette, leading to restoration of the GFP+ gene. By measuring the frequency of GFP+ cells, the function of DNA-PKcs in DNA repair is determined. Briefly, reporter plasmids are transfected into B7-H1-positive or -negative tumor cells, followed by treatment with one or more cytotoxic agents. The frequency of GFP+ cells is determined and compared between B7-H1-positive and negative-tumor cells using flow cytometry.

If B7-H1 in association with DNA-PKcs stimulates the DNA repair function of DNA-PKcs, expression of γH2AX (a sign of DNA DSBs) will decrease more slowly in B7-H1-positive tumor cells than in B7-H1-negative tumor cells, as a result of sufficient DNA repair by DNA-PKcs. Nuclear foci distributed throughout the nucleus are the most common distribution of γH2AX, but γH2AX expression at the nuclear periphery has been reported in early stage apoptotic cells (Solier et al., supra). Since DNA-PKcs also phosphorylates H2AX during apoptotic DNA fragmentation (Mukherjee et al., DNA Repair 5:575-590, 2006), the pattern of γH2AX distribution predicts whether B7-H1 regulates the function of DNA-PKcs in DNA repair or in DNA fragmentation.

Example 6—Defining the Role of B7-H1 Interaction with DNA-PKcs in the ERK/Bim Pathway

DNA-PKcs as a kinase activates Akt and ERK pro-survival signaling pathways (Dragoi et al., EMBO J 24:779-789, 2005; and (Yotsumoto et al., JImmunol 180:809-816, 2008). The direct effects of DNA-PKcs on ERK activation are not clear, however. When the relative phosphorylation levels of proteins involved in the MAPK/ERK pathway in B7-H1/624mel cells and Mock/624mel cells was evaluated using antibody arrays (R&D Systems, Minneapolis, Minn.), phosphorylation of mTOR (an element in Akt pathway) and RSK1/2 (an element in ERK pathway) were significantly increased among B7-H1/624mel cells compared with Mock/624mel cells (FIG. 8A). Accordingly, phosphorylation of ERK1/2 and GSK-3 (a downstream element of Akt; Bodine, Med Science Sports Exercise 38:1950-1957, 2006) also were increased. Since increased phosphorylation of Akt in the nucleus is associated with B7-H1 re-distribution to the nucleus (Ghebeh et al., supra), and because B7-H1 and DNA-PKcs co-localize in the nucleus (FIG. 6 ), it is possible that activation of Akt pathway could be regulated by DNA-PKcs in association with B7-H1. Increased ERK1/2 activation was confirmed by Western blotting (FIG. 8B) and an intracellular flow cytometry assay that showed a >2-fold increase of phospho-ERK1/2 (FIG. 8C). In both assays, total ERK levels remained comparable between B7-H1/624mel and Mock/624mel, suggesting that B7-H1 regulates the activation of ERK1/2 rather than the ERK1/2 protein level. Based on these data, it is possible that upon treatment with cytotoxic drugs, B7-H1 is recruited to the nucleus where it functions as a platform for DNA-PKcs to activate ERK and Akt signaling pathways thereby suppressing tumor cell apoptosis.

To test the role of DNA-PKcs in activation of the MAPK signal cascade, tumor cells were treated with NU7026, a DNA-PKcs specific inhibitor. The results shown in FIG. 9 demonstrate that NU7026 dramatically decreased (˜2-fold) the activation of ERK1/2 in B7-H1/624mel cells but not Mock/624mel cells, suggesting DNA-PKcs may be a positive regulator of ERK1/2, and that DNA-PKcs may require B7-H1 in activation of ERK1/2. As a mechanism of action of ERK1/2 in drug resistance, ERK1/2 phosphorylates Bim and enhances degradation of Bim in tumor cells (Gillings, et al., FEBS J 276:6050-6062, 2009; and Luciano et al., Oncogene 22:6785-6793, 2003). The findings shown in FIG. 9 suggested that B7-H1 in association with DNA-PKcs enhances the activation of ERK1/2 that promotes Bim degradation by phosphorylation, thus countering tumor cell apoptosis (diagrammed in FIG. 10 ).

To test this, the phosphorylation of Bim in the presence of DNA-PKcs inhibitor (NU7026) is examined in endogenous B7-H1-positive MDA-MB-231 human tumor cells (FIG. 7 ) following treatment with cytotoxic drugs. The IC50 for NU7026 to inhibit DNA-PKcs is 0.23 uM (while the IC50 for inhibition of PI3K is 13 uM). To specifically examine the effects of NU7026 on Bim phosphorylation, NU7026 is titrated gradually from 10 uM to 0.23 uM (using the same volume of DMSO solvent as a control). To further confirm the role of DNA-PKcs in Bim phosphorylation, DNA-PKcs knockout cell lines (Wu et al., J Immunol 174:934-941, 2005) or DNA-PKcs knockdown cell lines are used to measure the levels of ERK1/2 activation in the absence of DNA-PKcs proteins. In both cases, the ERK1/2 inhibitor U0126 (which inhibits MEK, an upstream kinase of ERK1/2) is used to confirm that phosphorylation of Bim is mediated by ERK1/2 activation. To specifically determine whether DNA-PKcs requires B7-H1 to regulate ERK1/2 activation and Bim phosphorylation, the effects of DNA-PKcs inhibitor are examined in B7-H1 knockdown tumor cells (FIG. 7 ). To measure phosphorylation of Bim, an electrophoretic mobility shift assay of Bim in Western blot is used (Luciano et al., supra; and O'Reilly et al., J Immunol 183:261-269, 2009). In this assay, phosphorylated Bim migrates more slowly than non-phosphorylated Bim. To confirm that the slower migrating band of Bim is due to phosphorylation of Bim, lysates are incubated with lambda phosphatase (λ-PPase, 15 ug/200 U for 1 h), which de-phosphorylates modified serine, threonine and tyrosine residues. To specifically identify the phosphorylation of Bim, an anti-phospho-Bim (Ser69 in human) antibody (Cell Signaling Tech. #4581) is used in a Western blotting assay, since phosphorylation of Bim at Ser69 by ERK/1/2 promotes Bim degradation (Luciano et al., supra). Total Bim also is measured to determine to what degree Bim is undergoing degradation. Accordingly, the apoptosis of tumor cells is measured by flow cytometry using antibody against activated caspase-3 as described in FIG. 1C.

Example 7—Defining the Role of B7-H1 Interaction with DNA-PKcs in Akt/Bad Pathway

DNA-PKcs enhances Akt activity (Dragoi et al., supra; and Feng et al., J Biol Chem 279:41189-41196, 2004). The increase of mTOR activation in B7-H1/624mel cells (FIG. 8A) and the association of B7-H1 with DNA-PKcs (FIGS. 2A-2C) suggest that Akt could be a downstream element in the B7-H1/DNA-PKcs pathway. Since activated Akt promotes cell survival by phosphorylating Bad, and blocks Bad-induced death (Datta et al., Cell 91:231-241, 1997; and del Peso et al., Science 278:687-689, 1997), it is possible that B7-H1 in association with DNA-PKcs enhances the activation of Akt that decreases Bad via phosphorylation, thus countering tumor cell apoptosis (FIG. 11 ). To test this hypothesis, the phosphorylation of Bad is examined in B7-H1 positive or negative tumor cells following treatment with cytotoxic agents in the presence of DNA-PKcs inhibitor (NU7026), or in DNA-PKcs knockout cells. In both cases, to confirm that activated Akt mediates the phosphorylation of Bad, the Akt inhibitor MK2206 (Merck) is used to directly inhibit the enzyme activity of activated Akt (Merck data sheet) in the studies. To specifically identify the phosphorylation of Bad, anti-phospho-Bad (Ser136) antibody (Cell Signaling Technology, clone 185D10) is used in a Western blotting assay, since Akt preferentially phosphorylates Bad at Ser136 in tumor cells (Hayakawa et al., Cancer Res 60:5988-5994, 2000). Phosphorylation of Bad could be mediated by activated ERK1/2, which phosphorylates Bad at Ser122; an anti-phospho-Bad (Ser122) antibody (Pierce-Antibodies) is used to test this possibility. Total Bad is measured to determine the degree of Bad degradation. If DNA-PKcs functions as an upstream regulator of Bad, reduced phosphorylation of Bad is identified in cells treated with DNA-PKcs inhibitor NU7026 or in cells without DNA-PKcs.

Taken together, these studies provide new insights for overcoming tumor chemoresistance, and a new direction for future combined chemotherapy and immunotherapy targeting B7-H1 expressed by aggressive or refractory human tumor cells.

Example 8—DNA-PKcs Activity is Required for Association of DNA-PKcs with B7-H1

B7-H1 positive human breast cancer cells (MBA-MD-231) were used to examine the association of DNA-PKcs and B7-H1. Immuno-precipitation assays showed that NU7026, an inhibitor of DNA-PKCs, abolished the association of B7-H1 with DNA-PKcs (FIG. 15A), while immunofluorescence staining showed that doxorubicin-induced co-localization of B7-H1 and DNA-PKcs at the nucleus (FIG. 15B, arrow, upper right panel) was blocked by 1 μM NU7026 (lower right panel). The IC50 for inhibiting DNA-PKcs activity is 0.23 μM.

Other Embodiments

It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims. 

1. A method for treating a cancer patient, said method comprising: (a) administering, to the cancer patient, a DNA-PKcs inhibitor, wherein said DNA-PKcs inhibitor is a small molecule or a polypeptide comprising a B7-H1 intracellular domain or a fragment thereof, and wherein said DNA-PKcs inhibitor inhibits interaction between B7-H1 and DNA-PKcs; and (b) administering, to the cancer patient, an anti-B7-H1 blocking antibody.
 2. The method of claim 1, wherein the cancer patient is a human. 3-4. (canceled)
 5. The method of claim 1, wherein the cancer is a melanoma cancer, a breast cancer, a lung cancer, a renal cell carcinoma cancer, a pancreas cancer, a prostate cancer, a colon cancer, a brain cancer, a liver cancer, or an ovarian cancer.
 6. The method of claim 1, wherein the DNA-PKcs inhibitor and the anti-B7-H1 blocking antibody are administered to the cancer patient simultaneously.
 7. The method of claim 1, wherein the DNA-PKcs inhibitor and the anti-B7-H1 blocking antibody are administered to the cancer patient sequentially. 8-14. (canceled) 